AMBER Archive (2008)

Subject: Re: AMBER: NAB to calcuate entropy. .

From: David A. Case (case_at_scripps.edu)
Date: Thu Feb 21 2008 - 11:10:36 CST

On Wed, Feb 20, 2008, Wang, Xuelin wrote:
>
> Here are the output, input pdb file and nab input file. I used a small
> DNA molecule to do testing. It works without using nsnb=99999. Is it
> right?

It is not "right", since you never succeeded in fully minimizing the molecule
before computing normal modes.

The "sample" code in the manual is just to get you started...you have to make
sure that you have enough minimization steps to get to a very low gradient
(say 10**-6, although I usually go to 10**-11 or so just to be sure.) You
will probably need many more conjugate gradient steps, or perhaps more
Newton-Raphson steps...it's hard to give universal formulas here. But you
need to work to get a good minimum before computing normal modes.

....dac

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu